Adjustment Period

Disclaimer: No, I don't own them, for which I should think they're profoundly grateful.

Summary: When John is forced to stay on Earth after the replicator attack, the SGC sends Sam Carter in his place.

Feedback: Yes please. Even if it's bad. Especially if it's bad.

"Why do we have to choose a new team leader?" Rodney grumbles. Well, grumbles is charitable, it's more like whines but Sam's trying to be charitable to him. To everyone on Atlantis, really; mainly because she thinks that if she isn't, she'll want to throttle a good half of them.

"Because I think, and Colonel Carter agrees, that the military commander should remain on base," Weir says, offering Sam a smile that doesn't fool her for a second. Weir has diplomatic polite down to a frighteningly fine art, but Sam's seen the better part of a decade's worth of diplomatic polite across more worlds than she can count, and she's not fooled.

Also: she does not, in fact, agree. She strongly disagrees, but Weir is in charge, and not the way she was in charge with Sheppard, where they were basically a team.

"Can't we just steal Lorne?" Rodney asks.

"Major Lorne has his own team," Weir says, frowning at him across the conference table.

"Hence, steal," Rodney says. He hasn't looked at Sam once since they all sat down, doesn't now, just glares at the screen of his data pad.

"Major Lorne isn't available for reassignment," she says, flicking her gaze over Teyla and Ronon as well, even though neither of them has said anything. "I can supply you with a list of potential team leaders, or I can choose one for you."

The three of them look at each other, and Sam's heart hurts. She misses her team, the way they could do that.

"We will choose someone from your list," Teyla says finally.

"By the end of the week, please," Weir puts in, and Teyla nods.

"Anything else?" Rodney demands. "Or can I get back to trying to save the city?"

"I'm not aware of the city being at risk at the moment," Weir says mildly. "But yes, you can all go back to work."

They file out, leaving Sam behind with Weir. "Do you need me for anything else?" Sam asks, and doesn't say ma'am, because Weir may be in charge, but she is not Sam's boss, she's not Sam's CO, and Sam's damned if she's going to let Weir have that.

She takes a deep breath, pushes calm over her frustration, over the urge to say, I wish he was here as well. I didn't ask for this.

There's an email waiting for her from Cam, when she goes back to her office: Daniel's still missing, they're still looking. He thinks Vala might run, try to find him on her own. He knows that Teal'c is talking to Jack, looking for advice, even though Teal'c denies it. He misses her, and wishes she was there.

She hears his voice in her head as she reads, and thinks, Me, too. There to look for Daniel, there to keep Vala from skipping off, there to get the truth from Teal'c and advice from Jack, there to say, You're doing fine, to Cam, even though she knows he won't believe her, he never does.

It doesn't sound the same by email, but she says it all anyway.

Sheppard's old team pick Major Eve Hatsford, newly arrived in Atlantis to replace someone who didn't want to come back after their exile on Earth, as their new team leader, and Sam calls her into the office to tell her.

Hatsford is nearly as tall as Ronon, slim and neat, black hair cut short around her dark face. She stands at ease in front of Sam's desk and just says, "Yes, ma'am," when Sam says that she's been assigned leader of Team One.

"They've been together for a couple of years," Sam adds, feeling like she should warn Hatsford, trying to remember how it felt when Cam stepped up in Jack's place in hers, except that she'd already given it up then. "There's going to be a period of adjustment."

"Yes, ma'am," Hatsford says again. She's looking at a point just above Sam's head typical marine, but she was SGC for two years before coming out, she knows her stuff. "Will there be anything else, ma'am?"

Sam wants to tell her that Ronon only stayed because of Sheppard; that Rodney hates everyone, and he'll hit on her while he hates her; that Teyla is polite and welcoming to everyone, but don't read into it. Instead, she says, "No, Major, thank you," and watches Hatsford leave.

Everyone expected that Sheppard would go back to Atlantis as soon as the expedition got reactivated. Sam didn't even think about Daniel had only been missing for a few days, she hadn't had the mental space to think about anything but him.

Cam, who tends to know these things, said that General Landry wanted Sheppard punished for stealing the jumper and disobeying an order, and that Jack, who'd stepped up for him a couple of times already, couldn't do it again. But Sheppard had rescued him and Woolsey, so Sheppard only lost Atlantis, not his commission or the SGC.

Her last night on Earth, she made a weak joke to Cam about swapping her for Sheppard on SG1. He didn't laugh, just shook his head and looked awkward, and she wondered. Still wonders and won't ask, not when the only way she has to speak to him is through email.

She asks about Cassie instead, and says, Tell her I miss her, instead of Tell her I feel guilty for being one more person who left her.

Hatsford's first mission with Team One they've always called the teams by their leader's name, but they do have designations, and Sam's going to use them, if only so people will stop saying "Sheppard's team" is to a planet that the Athosians know, which is supposed to have some kind of big superhero.

"I'd like to send Dr Beckett with the team," Weir says as Sam goes through the week's mission roster with her. "He still doesn't have much off-world experience, but his medical skills could be valuable in opening up a trade agreement."

"No," Sam says. For a second, she sees Janet's body, before she blinks it away.

"Excuse me?" Weir asks, one eyebrow going up.

"You said it yourself, he doesn't have much off-world experience," Sam points out. "And we don't know what this superhero is about sending an inexperienced civilian into something like that could be asking for trouble."

"He was part of the mission to take back Atlantis from the replicators," Weir says mildly, the unspoken As was I clear enough.

"That doesn't make this a good idea," Sam says carefully. "I won't agree to it."

Of course, Weir can over-ride her. When Weir looks down, taps her pen against the desk, that's what Sam expects. Instead, she looks back up and says, "If that's what you think best."

"It is," Sam says, and bites down on the small smile of victory she can feel trying to edge onto her face.

The team comes back quiet, and when Sam asks what happened, Hatsford comes to attention, right there on the gate room floor, gives a report that skates through Kolya and Lavin and imprisonment, Hatsford and Ronon breaking them out of the cell, incapacitating their captors for the run back to the gate.

"Commander Kolya?" Weir asks. Sam doesn't look at her, hearing the faint tremor in her voice. She's read the reports read Weir's report of the siege, like something out of a comic book, and Sheppard's shot that saved her and terrified her at the same time.

"We weren't able to verify, but I believe he's dead," Hatsford says. She doesn't blink, but then she doesn't need to Rodney looks at Ronon with gratitude splashed all over his face.

"That’s all for now," Sam says, before anyone can say anything that someone will regret. "Get down to medical. Written reports in forty-eight hours."

She doesn't want to bond with Weir, doesn't want Weir to confide in her. She isn't sure what she does want, but she knows it isn't that, some parody of a chick flick moment, but with uniforms and weapons.

"Of course," Weir says, and even if the word isn't there, the tone of dismissal still is.

She emails Cam and writes Tell Sheppard that Kolya's dead. It's the closest she can safely get to the question she won't ask until she's back on Earth and can ask it in Cam's apartment with an empty wine bottle between them.

Cam's next email talks about the search for Daniel, about running into Tomin, and at the very end just says Thanks.

Atlantis has three O-4s: Hatsford, Maine and Lorne. They also have incredibly bad luck with them, so Lorne's defaulted into military second-in-command, by virtue of being the only person of appropriate rank not to have died, been sent home, gone crazy, or gotten lost in Pegasus somewhere.

"That doesn't worry you?" she asks, when he explains it to her pretty much exactly like that, sitting on the other side of her desk and grinning wryly at her.

He shrugs. "I think it worries the others more than me. Henderson started a rumor that I was blessed by an Unas back in the Milky Way, and that's why I'm the only surviving major in the city."

He stands up, pours more coffee for both of them without asking, and it's nice nice to be treated like a friend, like a colleague, instead of like a boss or an intruder or someone who needs to be coddled, treated politely.

Of course, it probably doesn't hurt that when they met they *were* equals, even if it wasn't for very long.

"Is McKay all right?" she asks, when he sits down again and hands over her coffee.

He shrugs again. "Dr Beckett's keeping him in overnight, but he seems fine. Babbling away about how he had the brilliant idea to save himself from ascending."

"Nothing to do with Teyla's meditation training that let him get to that point in the first place?" Sam asks dryly.

"Purely his genius brain," Lorne concurs, straight-faced.

"That's what I figured," Sam agrees. That's another reason she likes having him around he's maybe the only person she has regular contact with who doesn't give her the big, betrayed eyes if she says something less that complimentary about their head of science. She gets that it's an insider thing no-one hits my brother but me and that Rodney's changed since he came to Atlantis, but he's still the guy who sometimes makes her want to snap her fingers, say, "My eyes are up here, actually."

"You get used to it," Lorne says, resigned, and the thing that worries Sam is, she knows that's true, and she does not want to.

Lorne thinks the whole thing with Geldar, and Rodney being their god, is hilarious.

Sam really doesn't.

"You modeled your supposedly fictional leader after me?" she demands, sitting around the conference table, trying not to shout loudly enough for the gate techs to hear her.

"It's a compliment," Rodney says, completely unashamed. "She's beautiful, smart, leader of her people just like you. Well, except for the leader of her people part, unless you consider the military to be your people, which I suppose you probably do."

"First the half-naked fantasies when you're drowning, now you're modeling some poor woman into a copy of me." Sam tries to take a deep breath and be calm be the military leader but she just can't get there. "What's next, am I going to find your shrine to me or something?"

"Why would I build you a shrine?" Rodney asks, sounding genuinely curious.

"Because you're behaving like the kind of creepy stalker who would!" Sam snaps.

"All right," Weir says calmly, raising a hand to both of them. "I think we've wandered a little off the point of this meeting."

She starts talking again, about negotiating a peace between the two nations, but Sam's only half-listening. She can almost feel the vibrations of anger and adrenaline skipping in her blood, and it just makes her more angry, more annoyed, because this is Rodney, he's harmless, not a threat.

She doesn't want to think about what some of the marines are probably saying about this behind her back. The blonde, female Air Force lieutenant colonel who got slid into the place of their beloved leader, who's as much a scientist as she is an officer and never goes off-world… She can just imagine the rumors, and now she's got Rodney making it worse with his stupid fantasies, his stupid game. She knows the whole thing will spread like wild fire through the city, and she's got no choice but to stick it out until something more interesting happens.

For one incredibly petty moment, she wishes it was Rodney getting laughed at behind his back, humiliated in front of his peers at least he's done something for it.

The negotiations go…not as well as might have been expected, and Rodney hovers, says, "Couldn't we just," and, "Maybe we should," long after Sam stops giving him a reason for why they can't and they shouldn't.

"I feel like I should take some responsibility for this," Rodney says finally.

"You should," Sam agrees, giving him her best fake smile. "You and Sheppard both, you should have known better than to mess with something like that without checking it out in the database first. But let Dr Weir do her job."

"I don't think " Rodney starts, frowning.

"Rodney," Sam says, low and warning.

"I wasn't " Rodney protests immediately. "I'm sure Elizabeth is doing her best, I'm just saying Sheppard and I pushed them pretty hard, and I don't know that . Anyway, I thought you didn't like her."

Sam's not touching that one not in her own head, and certainly not for Rodney's benefit. "Do you see these files?" she asks, gesturing to the two piles, and whoever said Atlantis was a paperless city has clearly never been there. "They're work that I have to get done. Preferably today."

"Do you want me to leave?" Rodney asks.

Sam closes her eyes and channels General Hammond at his most calm. "Yes, Rodney, I want you to leave."

To her surprise, he does.

It seems like the negotiations are going to fall apart, like Geldar's and Hallona's planet is going to be one more place that's worse off for Earth's interference, but Weir is nothing if not a consummate professional and brilliant diplomat, and she manages to send them through the gate with a tentative peace agreement.

Sam's on her way to the gate-room to offer her congratulations when Lorne's team step out of the locker room, nearly bowling her over. "Sorry, ma'am," Henderson says, one hand brushing her elbow as he steadies her. "Didn't see you there."

"Well, sure," Henderson starts, and Sam looks a question at Lorne - was that you? - but just gets a shrug in return.

Weir's waiting on the balcony when they get to the gate-room, so Sam joins her to wave the team off. Weir doesn't look over at her, so Sam stands next to her, watches Lorne pat Parrish down the way Jack used to with Daniel when they first started going through the gate. "Seems like someone's quashed the part about Rodney modeling Nola in my image," she says.

"I would think that's for the best," Weir says. "I wouldn't want the respect people have for you as military commander to be undermined."

"No," Sam agrees. She hesitates, wonders if she should say thank you. It doesn't feel right, not when the silence is, for once, comfortable.

"I hear you put up a spirited defense of my skills to Rodney earlier," Weir adds, still watching the action on the gate-room floor.

Sam feels her face flush, stupidly. "It was all true," she says.

Weir finally looks over. "Thank you, all the same," she says.

A week later, when Sam's finishing up running through the mission roster with her, Weir looks up and says, "If you think that you could fit it in amongst your other duties, I'd like to assign you to work with the team on the planet-wide anti-replicator weapon."

Sam swallows down the first thing she wants to say there's an actual project working on that? - and says, "I'm not sure how the current research team will feel about that."

Weir gives her a small, knowing smile. "And by research team, you mean Rodney McKay?"

Sam risks a smile back. "Something like that."

"It's being handed over from Area 51 to Dr Zelenka, and the only person who can assign the military commander is the civilian commander," Weir says. "Also, they need an expert in the replicators."

"Lucky we have one in the city then," Sam says, and means Thanks.

She doesn't tell Cam that she's got a scientific assignment, and doesn't think too hard about why she isn't telling him. She knows, from him, that Sheppard's been made co-commander of SG2 after a newly promoted lieutenant colonel got put in charge, and she can only imagine how Sheppard feels about that.

She tries not to imagine how awkward the 'no, not like that,' conversation will be if she's wrong.

She thinks she probably doesn't need to worry about it.

For a few weeks, Atlantis is good: the project goes well, starts to make real progress, Weir starts to treat her more like a competent professional and less like an interloper, and she stops feeling like half of her marines are mentally comparing her to Sheppard and finding her wanting.

Then Dr Beckett, Corporal Filton, and Dr Hewston are killed.

She doesn't didn't know any of them well, but that hardly matters. Filton was one of her marines, and they died in her city, from a threat that she didn't effectively protect them from.

"I'd like to go back to Earth with Carson's with Carson," Weir says, sitting very straight in her office as they go through the memorial processes. She has dark circles under her eyes, and Sam wants to say, It's not your fault, except that, if she feels guilty, it's stupid to expect that Weir wouldn't.

"Of course," she says instead. "Will you go to Scotland with him?"

Weir shakes her head. "The IOA have asked me to make myself available for a couple of days, since I'll be on Earth anyway." She smiles wryly.

"We'll keep the place running smoothly without you," Sam promises.

In an effort to save power, the SGC decides to keep all six pall bearers and send them back together, a decision of which Sam is not in favor, since it pretty much wipes out the command element, military, civilian and scientific.

She makes Hatsford her temporary second-in-command, since she's temporarily in overall command, and resigns herself to the better part of a week on not much sleep. Even if she's not sleeping all that well, it doesn't exactly fill her with joy.

Which means that, when Teyla knocks on Weir's office door the morning after Beckett and the others went back to Earth, and says, "I wish to offer you any assistance I can give," Sam practically bites her hand off saying yes.

They're a good team, her and Teyla and Major Hatsford. For a week, they pull marines into line, wrangle scientists, supervise the rebuilding of the damaged medical corridors, reassure and calm and organize, and when Weir comes back, she looks around the gate-room and says, "You cleaned!" looking amused and better than she has since before the explosions.

"We didn't want you to come back to an untidy city," Sam says, mentally patting herself and her team on the back. No dramas, no crises, and now they've made the civilian commander smile. She adds why the latter matters more to her than the first two to her list of things that she's not thinking about.

"And I appreciate it," Weir says. "Thank you, all of you, for stepping up when we needed you." No-one says anything, and Weir's smile becomes slightly forced. "I'd like to catch up with you on what I missed. Perhaps in my office after dinner. I brought chocolate cake from Earth."

"Well, if there's cake," Sam says, grinning, and even Hatsford nods.

As it turns out, Weir brought more than cake she also brought a bottle of good red wine.

Of course, she didn't bring a cork screw or actual wine glasses, and so they end up using Hatsford's pocket knife to open it, and pouring the wine into coffee mugs. Hatsford hesitates when Weir holds one out to her, looking at Sam, who nods. "Take it. We're off-duty, I think."

"You are," Weir assures them. "You don't have to drink if you don't want to, Eve, but you're not here as a marine."

"I'm always a marine," Hatsford says, but she doesn't add 'ma'am,' which Sam thinks is probably as close to off-duty and relaxed as she ever gets.

She still only drinks half of her cup of wine, slowly, over the course of the conversation, and excuses herself as soon as it's polite to do so.

"She seems very competent," Weir says, watching her move across the gate-room, checking on the duty techs as she goes.

"She is an excellent team leader," Teyla adds. She's slumped, very slightly, back in her chair, and Sam thinks the wine is hitting her hardest. "She is very efficient. Ronon likes her a great deal, though I am not sure that Rodney does."

Sam would just bet Rodney doesn't like her that much. She can't imagine Hatsford putting up with him when he gets paranoid and alarmist.

"She's a great asset to the city," Sam says. "I think it might be time to reshuffle some of the roles here make the second in command a split post, one for off-world missions and one for internal."

"You do what you think is best," Weir says, and Sam feels warm from more than just the wine.

Sam dislikes Colonel Ellis from the moment he beams into her city without even waiting for permission, even though it's standard procedure to get approval before beaming.

She likes him even less when he sweeps in and starts talking to her and Weir as though there's no problem with the SGC having kept the existence of ships on the replicator homeworld a secret from them for three weeks.

On the other hand, when McKay points out that six nukes is going to be about as effective as a fly-swatter on the replicator ships, and Ellis says, "That’s more than enough to slow them down, for now," she gets a serious kick out of being able to say:

"Actually, I think we might have a better solution."

And an even bigger kick out of pointing a weapon that she helped design at a planet full of beings intent on destroying everyone and everything she cares about, and seeing it fall apart. Literally.

"What do you call that thing again?" Ellis asks.

"Planet wide anti-replicator weapon," Sam says airily. "Just something the research team and I have been working on in our spare time."

"Nice hobby," Ellis says, grudgingly impressed.

Dr Weir is waiting for them when they get back to the city. "Did it work?"

"Like a charm," Sam confirms.

"Good work, Colonel," Weir says warmly, falling into step next to her in a way that neatly blocks Ellis from the conversation. "Now let's talk about finding a way to do the same thing to the Wraith, shall we?"

"Yes, ma'am," Sam says, and the honorific feels natural feels right as she says it.